Zhao identified and experimentally confirmed a pyridoxal-phosphate derivative, which create a covalent linkage of the pyridoxal-phosphate moiety to the residue Lys120 in the binding groove of the 14-3-3 protein17,18. the inhibitors and the hydrophilic residues. To improve the binding free energy of Rx group, we designed the inhibitor R9 with group R9?=?4-hydroxypheny. However, we also found that the binding free energy of inhibitor R9 is smaller than that of inhibitor R1. By further using the steer molecular dynamics (SMD) simulations, we identified a new hydrogen bond between the inhibitor R8 and residue Arg64 in the pulling paths. The information obtained from this study may be valuable for future rational design of novel inhibitors, and provide better structural understanding of inhibitor binding to 14-3-3 proteins. Protein-protein interactions (PPIs) are important features for biological processes, and alterations in PPIs events could cause diseases such as cancer and diabetes1,2. Different proteins may have different interactions between each other3. A specific kind of PPIs describes that a protein can interact with parts of other proteins, peptides or small molecules which are termed as the inhibitors of the protein. This protein usually plays a role of the drug target. A rich source of potential drug targets offer attractive opportunities for restorative intervention by dealing with of PPIs with small, drug-like molecules. The 14-3-3 proteins are a family of ubiquitous conserved eukaryotic regulatory molecules involved in the rules of mitogenic signal transduction, apoptotic cell death, and cell cycle control4. This protein family consists of seven unique isoforms in human being cells (, ?, , , , and ) as well as a variety of post-translationally revised forms5,6. The 14-3-3 proteins have the ability to bind a multitude of functionally varied signaling proteins, ST 101(ZSET1446) including kinases, phosphatases, and transmembrane ST 101(ZSET1446) receptors. They mediate their SF1 physiological effects by binding to additional proteins, modulating their (clients) subcellular localization, enzymatic activity, or their ability to interact with further proteins7. For example, the isoform has been implicated in breast tumor8 and is necessary for proper G2 checkpoint function9. As one of the most important hub proteins with at least 200C300 connection partners, the 14-3-3 proteins are an especially productive case for PPI treatment10. Each 14-3-3 proteins consists of characteristic cup-like shape practical dimers with each monomer offers nine antiparallel -helices showing a so-called amphipathic groove that accommodates the mostly phosphorylated connection motifs of their partner proteins (observe Fig. 1A)11,12. ST 101(ZSET1446) Small-molecule rules on PPIs is one of the most fascinating but also hard fields in drug development and chemical biology13. Open in a separate window Number 1 (A) Initial structure of the 14-3-3 protein and its inhibitors. The two identical chains of the dimer are demonstrated in reddish and blue color, respectively. Helices are demonstrated as labeled cylinders. The inhibitors are demonstrated in large ball representation. The key residues are demonstrated in ball and stick representation. (B) Molecular constructions of eight inhibitors of the 14-3-3 protein. Previously, several attempts have been made to develop small-molecule inhibitors for the 14-3-3 PPIs. For example, Wu designed and synthesized a peptide-small-molecule cross library based on the original optimal 14-3-3 binding peptide and managed the central phosphoserine residue14,15. Corradi used an structure-based inhibitor design approach to determine the 1st non-peptidic small molecule compounds with anti-proliferative activity16. Zhao recognized and experimentally confirmed a pyridoxal-phosphate derivative, which develop a covalent linkage of the pyridoxal-phosphate moiety to the residue Lys120 in the binding groove of the 14-3-3 protein17,18. Bier reported a molecular tweezers which bind to a ST 101(ZSET1446) 14-3-3 adapter protein and modulate its connection with the partner proteins19. Thiel recognized noncovalent and non-peptideic small-molecule inhibitors for extracellular 14-3-3 PPIs by virtual testing20. In the work by Thiel were used as the starting constructions in our MD simulations20. Missing loops were from the crystal structure of 14-3-3 (PDB ID: 3MHR)55. All crystallographic water molecules were retained in the starting model. The standard AMBER push field (FF03)56 was used to describe the protein guidelines and water molecules. Single-point calculations with Gaussion 03 were performed to obtain the electrostatic potential around each compound by using Hartree-Fock/6-31?G* basis arranged57. Atomic partial charges of the inhibitors were fitted to the electrostatic potential (ESP) with this study by using the RESP method with the Antechamber module of AMBER12 package58. All compounds were solvated inside a rectangular periodic box of TIP3P59 water molecules having a margin distance.
